You can do it using one of the other hardware timers, but its non-trivial. Its easy to get a specific frequency going, but then you have to have the PWM line high or low for a specific duty cycle within that frequency, and of course the two lines are going to be set to different values.
You have two other options...
- switch to AVR - the ATmega168 has six hardware PWM pins, in the same size package
- use an external motor driver (assuming you're driving a motor) that has a serial interface, like the Sabertooth or whatever.